Use e2proc2d.py script to bin the super-resolution movie file

[王宁]

Hi everyone,

      I have a question about how to use e2proc2d.py script to bin the movie file with tif format,  to generate the mrc format file finally. I know that someone suggested to use this script, however, I don't know how to use the option for image bin.  Here is my command: 

e2proc2d.py  **.tif  **.mrc --medianshrink 2,   I want to bin 2 for movie files.  Is it right? any suggestions are wellcome, thanks advance!

  Ning

[Ludtke, Steven J.]

Start with

e2proc2d.py --help

mirroring one of the examples in the help:

e2proc2d.py *.tif @.mrcs --medianshrink 2

".mrcs" rather than ".mrc" is necessary to tell EMAN2 that you intend the MRC file to contain a stack of 2-D images rather than a 3-D volume. The contents of the file are identical in the 2 cases, and you can freely rename the .mrcs files to .mrc later if you like.

There are 3 methods for downsampling data:

--medianshrink  (performs a block median filter)

--meanshrink (perfoms a block average)

--fouriershrink (downsamples by Fourier truncation)

for most purposes --fouriershrink is probably the best choice as it will prevent aliasing of high frequency components back into lower resolution, but there are also arguments to be made for the other two methods.

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

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[王宁]

Thanks for your detailed suggestions. I just use the mrc file to train the topaz denoised model. Yes, it works!  

Best wishes,

Ning